Backed by Fretilin, the party that led the revolutionary struggle to the country's independence, Francisco "Lu-Olo" Guterres was leading with 59.24 per cent of votes.

But only 34.34 per cent of votes had been counted by early Tuesday, reflecting huge logistical problems in the largely mountainous country with a poor road network.

In previous elections, UN helicopters were used to ferry ballot boxes from the most remote polling stations.

Despite that voting was not compulsory, hundreds of thousands of Timorese waited patiently in long queues in blistering heat to vote for a new president for a five year-term ahead of general elections in July.

The elections will be a key to the future of Asia's newest democracy amid concerns the half-island nation's oil and gas revenues are rapidly running dry.

Running second in the early vote count with 30.06 per cent was Democratic Party politician Antonio da Conceicao, the 53 year-old current education minister who says he represents a younger generation of Timorese demanding a change of leadership in the country where poverty remains endemic and there are growing concerns about corruption.

Mr da Conceicao ran a strong anti-corruption campaign that seemed to resonate with many voters.

He also campaigned to the build the nation "from the grass roots" by ensuring the majority of people who live in rural areas have enough food, access to markets, schools, clinics, and water and sanitation.

Mr Guterres,62, will need to get more than 50 per cent of the vote to avoid a run-off election in April.

He is backed by the country's behind-the-scenes powerbroker and independence hero Xanana Gusmao, a former president and prime minister who created a government of national unity two years ago.

The president is largely a ceremonial post but the incumbent Jose Maria de Vasconcelos, who is known as "Taur Matan Ruak" has spoken out about corruption and insisted on revision of the government's budget.

Mr Vasconcelos is expected to contest the July elections for the newly formed People's Liberation Party (PLP), aiming to take the even more powerful position of prime minister who is appointed by 65 elected MPs.

East Timor has 744,613 registered voters in a population of 1.261 million.